Micromolecules

Micromolecules: definitions & links Cellular domains: Genome, preoteome & metabolome
Metabolic diversity: Scale, dynamics, & phyletics Phenotyping strategies: proteomics vs metabolomics
CMP Platforms: Platforms and workflow overview CMP Probes: The probe library
CMP Substrates: Molecular trapping & detection CMP Datasets: Data arrays for multichannel imaging
CMP Analysis: pattern recognition theory and tools CMP Exploration: N-space visualization tools
CMP Annotation: browsing & annotating data

 

Micromolecules Links and Tools
Unique cell classes can be distinguished by their small molecule ormicromolecular signatures. Micromolecules include elements and their molecular forms (e.g. O<font-size=8pt>2), ions, inorganic compounds, organic species formed by group transfer and oligomers formed by ligation reactions (e.g. glutathione). Signatures are partial representations of formal metabolic phenotypes, track physiologic and pathologic metabolic transformations, and can identify novel cell classes. Computational signature visualization in complex heterocellular tissues of all eukaryotic Kingdoms (Plantae, Fungae, and Animalia) reveals unexpectedly diverse metabolic phenotypes across cell classes. Metabolic phenotypes are challenging to interpret, as they arise from genetic and epigenetic demands: maintaining group transfer potentials for molecular synthesis, vectorial molecular transport processes, osmoregulation, redox and reactive oxygen species control, energetics regulation, intercellular signaling and coupling, cell and tissue growth, and protein synthesis. Though no coherent theory of metabolic differentiation predicts these phenotypes, once visualized, micromolecular phenotypes inform models and constrain modes of pharmacologic intervention. Visualizing signatures, tracking phenotype dynamics, and screening molecular interventions all require quantitative micromolecular profiling across cell classes. These measures can be uniquely acquired via Computational Molecular Phenotyping (CMP) with anti-hapten IgG libraries.  Metabolism
KEGG
PUMA2
Roche Appl Biosci Pathways via ExPASy
European Bioinformatics Inst (EBI)
BRENDA
HMDAMolecules
KLOTHO
LIGAND
Ligands-EBI
U West Indies Mona

Tools
RasMol
Chime
iMol for OS X
Gepasi: metabolic simulation

 

CMP Targets for Metabolomics Technology Development
Aliphatics
  1. 3-phospho-serine
  2. phospho-ethanolamine
  3. Ethanolamine
  4. Putrescine
  5. Ac Putrescine
  6. Spermine
  7. N-Ac Spermine
  8. Spermidine
  9. N-Ac Spermidine
  10. cadaverine
  11. carnitine
  12. dimethylglycine
  13. betaine
  14. N-Ac glutamate
  15. N-Ac asp-glutamate
  16. N-Ac lysine
  17. N-carbamoyl asp
  18. 5-aminovalerate
  19. oxo-5-aminovalerate
  20. L-arginine-phosphate
  21. L-arginosuccinate
  22. carbamate
  23. carbamoyl phosphate
  24. carbamoyl sarcosine
  25. sarcosine
  26. trimethyllysine
  27. 2-aminoadipate
Aromatics
  1. epinephrine
  2. histamine
  3. kynurenine
  4. melatonin
  5. tyramine
  6. monoiodotyrosine
  7. diiodotyrosine T2
  8. triiodotyrosine T3
  9. tetraiodotyrosineT4
ROS Molecules
  1. glutathione (red)
  2. glutathione (ox)
  3. cysteinylglycine
  4. gamma-glutamylcysteine
Nucleics
  1. Adenine
  2. Adenosine
  3. dAdenosine
  4. AMP
  5. dAMP
  6. dADP
  7. dATP
  8. S-AM
  9. Cytidine
  10. Cytosine
  11. dCytosine
  12. CMP
  13. CDP
  14. CTP
  15. dCMP
  16. dCDP
  17. dCTP
  18. Guanine
  19. Guanosine
  20. GMP
  21. GDP
  22. GTP
  23. dGMP
  24. dGDP
  25. dGTP
  26. GDP-mannose
  27. GDP-fucose
  28. Uracil
  29. Uridine
  30. UMP
  31. UDP
  32. UTP
  33. dUMP
  34. dUDP
  35. dUTP
  36. UDP-glucose
  37. Thymine
  38. dThymidine
  39. dTMP
  40. dTDP
  41. dTTP
  42. NAD / NADH
  43. NADP / NADPH
  44. aminoacylAMP
  45. allantoin
  46. allantoate
  47. Urate
Carboxylates
  1. Pyruvic acid
  2. 3-phosphoglycerate
  3. 2-phosphoglycerate
  4. glycerate
  5. succinate
  6. oxalacetate
  7. malate
  8. fumarate
Metabolite analogues
  1. D-alanine
  2. D-asparagine
  3. D-cysteine
  4. D-serine
  5. canavanine
  6. 1-amino-2-oxo-guanidopropane
  7. aminoisobutyrate
  8. isoguvacine
Sugars
  1. D-glucose
  2. D-glucuronate
  3. D-6-phospholuconate
  4. myo-inositol
  5. inositol-1-PP,
  6. inositol-1,4-PP,
  7. inositol-1,4,5-PP,
Cofactors
  1. CoASH
  2. Acetyl CoA
  3. Succinyl CoA
  4. Folate
  5. Tetrahydrofolate
  6. Formyl THF
  7. Methylenyl THF
  8. THF polyglu
  9. THB
  10. DHB
  11. Thiamine
  12. Thiamine-PP
  13. FAD
  14. FMN
  15. Pyridoxamine
  16. Cobalamin
  17. Pantothenate
  18. Biotin
  19. Quinolinate
  20. Ascorbate
Steroids / Precursors
  1. Mevalonate
  2. Mevalonate 5P,PP
  3. Testosterone
  4. Estradiol
  5. Estrogen
  6. Progesterone
  7. Cortisol
  8. Dihdroxycalciferol
Bilins, Bile Acids
  1. Porphobilinogen
  2. Uroporphyrins
  3. Heme
  4. Cytochromes
  5. Urobilins
  6. Stercobilins
  7. Bilirubin
  8. Bilirubin glucuronides
  9. Glycocholate
  10. Cholate
  11. Taurocholate
Eicosanoids
  1. Arachidonate
  2. Prostaglandins
  3. Leukotrienes
  4. Leukotriene C4
Polyketides / peptides
  1. Penicillins
  2. Cephalosporin
  3. Streptomycin
  4. Oxytetracycline
  5. creatine
  6. creatine-P